<p><i>Staphylococcus aureus</i> (<i>S. aureus</i>)-induced osteomyelitis remains challenging in clinical practice, wherein macrophages with impaired bactericidal function serve as reservoirs for intracellular bacterial survival, contributing to persistent and relapsing infections. Here, we show that exogenous manganese (Mn²⁺) enhances the bactericidal capacity of <i>S. aureus</i>-infected macrophages. By repressing the mitochondrial protein Sirt3, Mn²⁺ inhibits <i>S. aureus</i>-induced mitophagy via the PTEN-induced kinase 1/parkin pathway, thereby boosting the production of mitochondrial reactive oxygen species to eradicate intracellular bacteria. Pharmacological activation or genetic overexpression of Sirt3 abolishes these effects, identifying this axis as a key molecular target of Mn²⁺. Based on this, we further develop a biomimetic nanotherapeutic system for targeted Mn²⁺ delivery. In a mouse model of osteomyelitis, this nanosystem precisely represses Sirt3 in macrophages within the infected medullary cavity, markedly reduces bacterial burden, and effectively alleviates bone destruction. Our findings implicate an immunomodulatory mechanism by which Mn²⁺ enhances macrophage bactericidal activity and develops a potent Mn²⁺-based metalloimmunotherapeutical strategy for <i>S. aureus</i>-induced osteomyelitis.</p>